Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:19:14 GMT 2023 |
| BAM file: | SRX7354307.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | strand-specific-reverse |
| Sorting performed: | yes |
Summary
Reads alignment
| Number of mapped reads (left/right): | 47,187,521 / 47,142,426 |
| Number of aligned pairs (without duplicates): | 47,137,633 |
| Total number of alignments: | 101,333,103 |
| Number of secondary alignments: | 7,003,156 |
| Number of non-unique alignments: | 10,355,728 |
| Aligned to genes: | 79,004,146 |
| Ambiguous alignments: | 276,424 |
| No feature assigned: | 10,498,987 |
| Missing chromosome in annotation: | 1,197,818 |
| Not aligned: | 9,256,473 |
Reads genomic origin
| Exonic: | 79,004,146 / 88.27% |
| Intronic: | 5,265,352 / 5.88% |
| Intergenic: | 5,233,635 / 5.85% |
| Intronic/intergenic overlapping exon: | 3,086,654 / 3.45% |
Transcript coverage profile
| 5' bias: | 0.56 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.81 |
Junction analysis
| Reads at junctions: | 28,092,846 |
| ACCT | 5.11% |
| AGGT | 4.73% |
| ATCT | 3.53% |
| AGGA | 3.48% |
| TCCT | 3.45% |
| GCCT | 3.31% |
| AGCT | 2.86% |
| CCCT | 2.69% |
| AGGC | 2.41% |
| TTCT | 2.22% |
| AGAT | 2.14% |
.png)
.png)
.png)
